If I am understanding the questiong, [AFAIK] I do not believe there is a way to flush the cache at runtime. However, by starting your application with the flag -clearPersistedState it will prevent the loading of any persisted application model. Or you can always delete the the workbench model from your workspace before you start.
Your/Workspace/Loc/.metadata/.plugins/org.eclipse.e4.workbench/workbench.xmi

Jeeeyul, I'm still not clear what the problem is. You uninstall an add-on on runtime and you get an error logged? What is the error? I think there's a cleanup addon around but I'm not sure if it deals with this case. If you describe the issue better (ideally file a bug on e4/runtime) we can take a look at it.

Application Model is serialized and deserialized when eclipse is launching. (E4Application#loadApplicationModel(IApplicationContext, IEclipseContext)

What if I uninstalled bundles which contributed Model Addons,
then Add-Ons which are contributed by uninstalled Contributor(Bundle) can be remains.
E4 Application can't resolve contributed URI(because there is no contributor), so it logs an error.